Development of a national proficiency test for SARS-CoV-2 detection by PCR in Colombia.

Background: Proficiency testing (PT) is a tool for ensuring the validity of results of testing laboratories and is essential when laboratories are working with assays authorised for emergency use or implementing novel techniques for detecting emerging pathogens. Methods: In collaboration with the National Health Institute of Colombia and with international support, we developed a qualitative PT for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse transcription polymerase chain reaction (RT-PCR). A proficiency test item (PTI) based on reference material (research grade) produced by the National Institute of Standards and Technologies (NIST) was prepared and characterised using three positive samples with varying concentrations of SARS-CoV-2 ribonucleic acid (RNA) and two negative (control) samples. Tests were distributed to 121 laboratories across the national network of public health laboratories in Colombia. Results: Positive samples had varying concentrations of SARS-CoV-2 RNA and were quantified by digital PCR (RT-ddPCR) assays for the E gene of SARS-CoV-2. We tested the ability of laboratories to detect low and high levels of viral RNA using samples with SARS-CoV-2 RNA concentrations of 1417 ± 216, 146 ± 28, and 14 ± 10 copies /uL (expanded uncertainty, k = 2, 95% confidence level) We also performed a semiquantitative analysis of instrumental responses (Ct values) reported by participating laboratories and homogeneity, stability, and characterisation studies of the produced materials to determine the adequacy of these materials and methods for use in the qualitative PT scheme. The PT evaluated reports for individual target genes from each laboratory; 98.3% of laboratories had satisfactory performance and the remaining 1.7% of laboratories had unsatisfactory performance for the detection of at least one of the reported genes. Conclusions: This PT scheme identified the potential metrological weaknesses of laboratories in the detection of SARS-CoV-2 by RT-PCR and may facilitate improvements in the quality of measurements from the perspective of public health surveillance.

[Phenotypic and genotypic diagnosis of bone and miliary tuberculosis in an HIV+ patient in Bogotá, Colombia]. / Diagnóstico genotípico y fenotípico de tuberculosis ósea y miliar en un paciente positivo para HIV en Bogotá, Colombia.

Tuberculosis is the single most frequent cause of death by an infectious agent worldwide. Diagnosis of extra-pulmonary tuberculosis is not always possible through conventional methods, due to the long time required for cultures and the paucibacillary nature of samples; hence the need of rapid molecular methods. HIV infection increases the risk of tuberculosis, and HIV/tuberculosis coinfection is associated with higher mortality. We describe the case of a 56-year old mestizo male patient suspected of having tuberculosis who consulted the San Ignacio Hospital in Bogotá with a two-month history of a painful ulcerated lesion over the distal third area of the right forearm and in whom HIV coinfection was confirmed. Bone and pulmonary histological examination evidenced multiple granulomas, giant cells and fibrosis. Cultures and IS6110-PCR from lung and bone tissues were positive for Mycobacterium tuberculosis complex. Mycobacterium tuberculosis isolates were sensitive to first line drugs.

Diagnóstico genotípico y fenotípico de tuberculosis ósea y miliar en un paciente positivo para HIV en Bogotá, Colombia / Phenotypic and genotypic diagnosis of bone and miliary tuberculosis in an HIV+ patient in Bogotá, Colombia

La tuberculosis se considera la causa más frecuente de muerte producida por un solo agente infeccioso. El diagnóstico de la tuberculosis extrapulmonar no siempre es posible mediante los métodos convencionales debido al lento crecimiento del bacilo y a la naturaleza paucibacilar de las muestras, por lo que es necesario recurrir a las técnicas moleculares. El riesgo de tuberculosis, así como la mortalidad, aumenta en los pacientes con infección por HIV, en quienes el compromiso extrapulmonar es más frecuente. Se describe el caso de un hombre mestizo de 56 años de edad con sospecha de padecer tuberculosis, que asistió a consulta en el Hospital San Ignacio de Bogotá y relató haber tenido dolor en una lesión ulcerada localizada en el tercio distal del antebrazo derecho durante los dos meses anteriores y en quien se confirmó la infección por HIV. El examen histológico de los tejidos óseo y pulmonar demostró la presencia de granulomas múltiples, células gigantes y fibrosis. Tanto los cultivos como la reacción en cadena de la polimerasa en la secuencia de inserción 6110 ( insertion sequence , IS6110) fueron positivos. Los aislamientos de Mycobacterium tuberculosis recuperados fueron sensibles a los medicamentos antituberculosos de primera línea.

Tuberculosis is the single most frequent cause of death by an infectious agent worldwide. Diagnosis of extra-pulmonary tuberculosis is not always possible through conventional methods, due to the long time required for cultures and the paucibacillary nature of samples; hence the need of rapid molecular methods. HIV infection increases the risk of tuberculosis, and HIV/tuberculosis coinfection is associated with higher mortality. We describe the case of a 56-year old mestizo male patient suspected of having tuberculosis who consulted the San Ignacio Hospital in Bogotá with a two-month history of a painful ulcerated lesion over the distal third area of the right forearm and in whom HIV coinfection was confirmed. Bone and pulmonary histological examination evidenced multiple granulomas, giant cells and fibrosis. Cultures and IS6110-PCR from lung and bone tissues were positive for Mycobacterium tuberculosis complex. Mycobacterium tuberculosis isolates were sensitive to first line drugs.

Necesidades metrológicas en los laboratorios clínicos / Metrological needs in clinical laboratories / Necessidades metrológicas nos laboratórios clínicos

Los resultados generados por los laboratorios clínicos son elementos claves para el diagnóstico y tratamiento de enfermedades, así como para el seguimiento de los pacientes, por lo tanto se requiere un control metrológico sobre el proceso de medición, el cual determinará el grado de comparabilidad y de confianza requerido sobre los resultados obtenidos. Esta revisión aborda el tema de comparabilidad de las mediciones y de cómo ésta se ve influenciada por factores como la conmutabilidad de los materiales de referencia, los métodos de medición, la disponibilidad de materiales y procedimientos de referencia, además de los intervalos de referencia y límites de decisión para un mensurando en particular. Finalmente se exponen cuáles son los mecanismos adoptados que permitirán garantizar la comparabilidad de las mediciones en esta área.

The results produced by clinical laboratories are key elements in the diagnosis and treatment of diseases and to monitor patients, so, it requires a metrological control over the measurement process, which will determine the degree of comparability and trust required on the obtained measurement results. Therefore, in this paper we discuss about the comparability of measurements and how it is influenced by factors such as commutability of reference materials, measurement methods, availability of materials and reference procedures, in addition to reference intervals and decision limits for a particular measurand. Finally it is exposed what are the mechanisms that allow ensure measurements comparability on this area.

Os resultados gerados pelos laboratórios clínicos são elementos chaves para o diagnóstico e tratamento de doenças, assim como para o seguimento dos pacientes, sendo preciso um controle metrológico sobre o processo de medição, que determina o grau de comparabilidade e confiança requerido sobre os resultados obtidos. Neste documento trata-se o tópico de comparabilidade das medições e de como a mesma se encontra influenciada por fatores como a comutatividade dos materiais de referência, os métodos de medição, a disponibilidade de materiais e procedimentos de referência, além dos intervalos de referência e limites de decisão para um mensurando em particular. Finalmente, são expostos quais são os mecanismos adotados que permitirão garantir a comparabilidade das medições nesta área.